rs9315915

Variant names:

• chr13-42422962-A-G
• rs9315915
• ENST00000637462.1:n.868+10910A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-42422962-A-G
• chr13-42422962-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637462.1(LINC02341):​n.868+10910A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.96 in 152,314 control chromosomes in the GnomAD database, including 70,333 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.96 (70333 hom., cov: 33)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448
• Publications: 1 publications found

Genes affected

LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02341	ENST00000637462.1	n.868+10910A>G		intron_variant	Intron 5 of 7	5

Frequencies

GnomAD3 genomes AF: 0.960 AC: 146123 AN: 152196 Hom.: 70301 Cov.: 33

Gnomad AFR AF: 0.883

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.970

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.960 AC: 146210 AN: 152314 Hom.: 70333 Cov.: 33 AF XY: 0.961 AC XY: 71537 AN XY: 74474

African (AFR) AF: 0.883 AC: 36670 AN: 41534

American (AMR) AF: 0.980 AC: 14995 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3461 AN: 3472

East Asian (EAS) AF: 0.958 AC: 4970 AN: 5190

South Asian (SAS) AF: 0.983 AC: 4742 AN: 4826

European-Finnish (FIN) AF: 0.995 AC: 10562 AN: 10620

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67561 AN: 68044

Other (OTH) AF: 0.970 AC: 2050 AN: 2114

Alfa AF: 0.976 Hom.: 10991

Bravo AF: 0.956

Asia WGS AF: 0.963 AC: 3350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9315915; hg19: chr13-42997098;